<?xml version='1.0' encoding='utf-8' ?>
<!DOCTYPE revhistory [

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%entities;
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<revhistory xmlns="http://docbook.org/ns/docbook" version="5.0">

  <revision>
    <revnumber>
      10.1.2
    </revnumber>

    <date>
      November 2025
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Full port of &MassXp; to the new &XpMass; project's libraries. Add new chapter on JavaScript features now in &MassXp;.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      7.0.0
    </revnumber>

    <date>
      November 2022
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The manual has not any content changed. Only this revision corresponds to
      a software bump matching a full code port to Qt6.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      6.1.0
    </revnumber>

    <date>
      October 2022
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Entirely reworked the user manual to make it more modern from the coding
      point of view. The users do not see any difference with the previous
      version.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      6.0.3
    </revnumber>

    <date>
      20210202
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Removed all mml elements (MathML) that made rendering the document too
      difficult. Replaced the formulae with figures. Adapted the text;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      5.7.0
    </revnumber>

    <date>
      20190115
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Finished porting of the historical LaTeX-based documentation to the
      DocBook/DAPS/FOP publishing system. Please, see Colophon for details;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20150918
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Update the manual to reflect the changes in the way ion product masses are
      computed in massXpert and update the various examples. Now, the
      fragmentation specification must produce fragments that are uncharged. The
      software will then ionize the/gc fragments using the ionization rule
      currently in use in the XpertEdit module;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20121205
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Update the manual to document the various new ways to import data in the
      m/z list in the XpertMiner module;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20111022
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Update the manual to describe the new fragmentation of oligomer containing
      cross-linked monomers feature;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20110829
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Update the manual to describe a number of new features;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20100429
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the section about the definition of monomers to document the new
      feature about computing the mass difference between any two monomers in
      the definition;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20100427
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the section about the cleavages of polymer sequences (XpertEdit
      chapter) to document the new feature that allows to only perform a
      cleavage in the currently selected region of a polymer sequence;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20090619
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the section about the chemical pad (XpertCalc chapter) to reflect
      improvements in the use of the chemical pad buttons (either immediate
      evaluation of the formula or mere insertion of the formula in the formula
      line edit widget);
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20090617
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the section about the chemical pad (XpertCalc chapter) to reflect
      improvements in the graphical display of the chemical pad buttons as
      programmed in the chem_pad.conf configuration files;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20090401
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Although not visible in the documentation, I wanted to publically extend
      my warm thanks to Lionel Élie Mamane, who helped me along these last
      months with the Debian packaging of massXpert. Note that this work also
      proved useful for other areas in the project.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20090220
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertEdit chapter to show how to configure the options about
      the number of decimals to be used for display of numerals in the program;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20090205
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertEdit chapter to show the simplified polymer sequence
      editing feature whereby editing of the sequence might be performed by
      clicking on monomer items in the list of all the monomers defined in the
      polymer chemistry definition. Fixed small bug in the documentation of
      about multi-region selection behaving as oligomers or residual chains.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20081211
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertEdit chapter to show the feature by which it is now
      possible to force the calculation engine to take into account the
      left/right end modification(s) when calculating the masses of a sequence
      region that does not encompass the left/right end of the polymer sequence.
      This new feature was essential in trying to perform full simulations of
      the molecular heterogeneity of the telokin protein (Rusconi et al. 1997
      Biochemistry). Added a paragraph about max count of chemical modifications
      of a given monomer at once in the XpertDef chapter and another one in the
      XpertEdit chapter to explain its working;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080911
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Finally indexed the whole document. Performed some minor modifications so
      that the documentation system does not produce HTML files anymore (the
      HTML production was not really worth it anyways);
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080805
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the user manual with a bunch of updated screen shots;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080730
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertMiner chapter to illustrate the m/z--z mass list matching
      feature;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080708
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertEdit chapter to illustrate the new multi-cleavage
      feature;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080701
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertEdit chapter to illustrate the new multi-region and
      multi-selection features;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080529
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Changed the install instructions for the Mac OS X system;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080527
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Added a chapter about XpertMiner to document the new features in that
      module. Some fixes here and there.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080526
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Modified the documentation to reflect switch to version 3 of the GNU
      General Public License;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080425
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The installation chapter was updated to illustrate the installation of the
      software in the Mac OS X system;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080424
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The installation chapter was updated to reflect the changes in the way the
      package might be installed (the package is now relocatable, provided the
      user indicates where the directories are located);
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080402
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertDef chapter was updated to detail the new way of defining
      fragmentation specifications where the side chain is decomposed in the
      gas-phase. The section about fragmentations is now much better documented;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080330
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a description of the new
      fragmentation/mass searching data in-place filtering. A section is now
      devoted to data filtering;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080325
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a description of the new
      sequence cleavage data in-place filtering;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080318
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a description of the find
      sequence motif feature;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080313
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a new paragraph about monomer
      cross-linking as this is now implemented in the software;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080221
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a new figure of the polymer
      modification procedure and to describe the enhanced modification
      procedure;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20080215
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The XpertEdit chapter was updated to include a new figure of the monomer
      modification procedure and to describe the enhanced modification
      procedure;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20071217
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The chapter about installation of massXpert has been rewritten to reflect
      changes in the building of massXpert and in the installation of Debian
      GNU/Linux and Fedora core GNU/Linux packages;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20071216
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The chapter about polymer chemistry definitions has been refactored to
      reflect the rewriting of the corresponding code. Added a small section
      about m/z ratio calculation, that was missing, although the feature was
      added a long time ago;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070922
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      The new multi-charged cleavage and fragmentation oligomers have been
      documented;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070819
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Switched back to version 2 of the GPL in the Appendices chapters, as
      massXpert cannot be licensed otherwise: the Qt libraries are licensed
      using version 2 of the GPL without the ``or any later version, at your
      option'' wording;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070728
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Updated the XpertDef chapter (modifications) to show the new ``targets''
      feature. Updated the XpertEdit chapter to show the new monomer
      modification dialog.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070719
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Added explanation on the arbitrary formula-based polymer sequence ends
      modification.
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070713
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Revision of the whole document for a better printed output;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070710
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Added a section to the XpertEdit chapter about the data mining mass list
      lab feature added recently. Mentioned the installation of Debian packages;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      20070630
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Switched the project and all accompanying documentation and other data
      files to GPL version 3;
    </revremark>
  </revision>

  <revision>
    <revnumber>
      not_set
    </revnumber>

    <date>
      2007 mid-june
    </date>

    <authorinitials>
      fr
    </authorinitials>

    <revremark>
      Start of the writing by taking inspiration of the GNU polyxmass manual.
    </revremark>
  </revision>
</revhistory>
